Did you notice if there were ANY standoffs under the motherboard, that did not line up specifically with a hole in the motherboard for a standoff screw to be installed though? Or in other words, are there any standoffs touching the bottom of the motherboard because they don't line up with a hole in the motherboard for a screw to go through?
Anything of that nature? Anything related to the installation of the motherboard itself that felt wrong, or off, or seemed peculiar, because I'm down to thinking this is related to something about the way the motherboard is installed since changing cases has affected the problem, and should not have, since disconnecting all of the front panel connections from the old case didn't change anything.
Glad you are having some success with games now though, at least.